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x-ray structure of methanol dehydrogenase from paracoccus denitrificans and molecular modeling of its interactions with cytochrome c-551i.the x-ray structure of methanol dehydrogenase (medh) from paracoccus denitrificans (medh-pd) was determined at 2.5 a resolution using molecular replacement based on the structure of medh from methylophilus methylotrophus w3a1 (medh-wa). the overall structures from the two bacteria are similar to each other except that the former has a longer c-terminal tail in each subunit and shows local differences in several insertion regions. the "x-ray sequence" of the segment alphagly444-alphaleu452 was es ...200314505072
effects of multiple ligand binding on kinetic isotope effects in pqq-dependent methanol dehydrogenase.the reaction of pqq-dependent methanol dehydrogenase (mdh) from methylophilus methylotrophus has been studied by steady-state and stopped-flow kinetic methods, with particular reference to multiple ligand binding and the kinetic isotope effect (kie) for pqq reduction. phenazine ethosulfate (pes; an artificial electron acceptor) and cyanide (a suppressant of endogenous activity), but not ammonium (an activator of mdh), compete for binding at the catalytic methanol-binding site. cyanide does not a ...200312667088
catalytic mechanism of dichloromethane dehalogenase from methylophilus sp. strain dm11.the glutathione (gsh)-dependent dichloromethane dehalogenase from methylophilus sp. strain dm11 catalyzes the dechlorination of ch(2)cl(2) to formaldehyde via a highly reactive, genotoxic intermediate, s-(chloromethyl)glutathione (gs-ch(2)cl). the catalytic mechanism of the enzyme toward a series of dihalomethane and monohaloethane substrates suggests that the initial addition of gsh to the alkylhalides is fast and that the rate-limiting step in turnover is the release of either the peptide prod ...200312974641
methylophilus quaylei sp. nov., a new aerobic obligately methylotrophic bacterium.a new obligately methylotrophic bacterium (strain mtt) with the ribulose monophosphate pathway of carbon assimilation is described. the isolate, utilizing only methanol, is an aerobic, gram-negative, asporogenous, non-motile short rod multiplying by binary fission. its cellular fatty acids profile consists primarily of straight-chain saturated c16:0 and unsaturated c16:l acids. the major ubiquinone is q-8. the dominant phospholipids are phosphatidylethanolamine and phosphatidylglycerol. diphosph ...200515997702
use of stable-isotope probing, full-cycle rrna analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community.a denitrifying microbial consortium was enriched in an anoxically operated, methanol-fed sequencing batch reactor (sbr) fed with a mineral salts medium containing methanol as the sole carbon source and nitrate as the electron acceptor. the sbr was inoculated with sludge from a biological nutrient removal activated sludge plant exhibiting good denitrification. the sbr denitrification rate improved from less than 0.02 mg of no(3)(-)-n mg of mixed-liquor volatile suspended solids (mlvss)(-1) h(-1) ...200414711691
extensive conformational sampling in a ternary electron transfer complex.here we report the crystal structures of a ternary electron transfer complex showing extensive motion at the protein interface. this physiological complex comprises the iron-sulfur flavoprotein trimethylamine dehydrogenase and electron transferring flavoprotein (etf) from methylophilus methylotrophus. in addition, we report the crystal structure of free etf. in the complex, electron density for the fad domain of etf is absent, indicating high mobility. positions for the fad domain are revealed b ...200312567183
histamine dehydrogenase from rhizobium sp.: gene cloning, expression in escherichia coli, characterization and application to histamine determination.the gene encoding histamine dehydrogenase in rhizobium sp. 4--9 has been cloned and overexpressed in escherichia coli. the coding region of the gene was 2,079 bp and encoded a protein of 693 amino acids with a calculated molecular mass of 76,732 da. this histamine dehydrogenase was related to histamine dehydrogenase from nocardioides simplex (54.5% identical), trimethylamine dehydrogenase from methylophilus methylotrophus (39.3% identical) and dimethylamine dehydrogenase from hyphomicrobium x (3 ...200515964650
detection of potentially novel bacterial components of the human skin microbiota using culture-independent molecular profiling.although the micro-organisms forming the cutaneous microbiota are considered to play important roles in the modification and prevention of skin diseases, a comprehensive analysis of their composition has not yet been carried out because of difficulties in determining yet-to-be-cultured micro-organisms in the samples. swab-scrubbed forehead skin samples of five healthy volunteers were analysed by profiling 16s rrna genes, as well as by conventional culture methods, to provide a profile of the cut ...200516278439
bacterial populations active in metabolism of c1 compounds in the sediment of lake washington, a freshwater lake.active members of the bacterial community in the sediment of lake washington, with special emphasis on c1 utilizers, were identified by employing two complementary culture-independent approaches: reverse transcription of environmental mrna and 16s rrna combined with pcr (rt-pcr) and stable-isotope probing (sip) of dna with the 13c-labeled c1 substrates methanol, methylamine, formaldehyde, and formate. analysis of rt-pcr-amplified fragments of 16s rrna-encoding genes revealed that gammaproteobact ...200516269723
[deuterium oxide as a stress factor to the methylotrophic bacterium methylophilus sp].the adaptation of the methylotrophic bacterium methylophilus sp. b-7741 to growth in highly deuterated media was studied. for the first time, we showed the cross adaptation of bacterial cells to deuterated media and oxidative and osmotic stresses. the activity at catalase in deuterated cells was higher than in the control cells. deuterated cell-free culture liquids showed protective effects on the growth of methylophilus sp. b-7741 in deuterated media, which was manifested as an increase in the ...200415198027
kinetic isotope effects and ligand binding in pqq-dependent methanol dehydrogenase.the reaction of pqq (2,7,9-tricarboxypyrroloquinoline quinone)-dependent mdh (methanol dehydrogenase) from methylophilus methylotrophus has been studied under steady-state conditions in the presence of an alternative activator [gee (glycine ethyl ester)] and compared with similar reactions performed with ammonium (used more generally as an activator in steady-state analysis of mdh). studies of initial velocity with methanol (protiated methanol, c1h3o1h) and [2h]methanol (deuteriated methanol, c2 ...200515617516
characterization of a unique mutant lyse gene, originating from corynebacterium glutamicum, encoding a product that induces l-lysine production in methylophilus methylotrophus.lyse24 is an allele of lyse encoding an l-lysine exporter of corynebacterium glutamicum. the mutant gene is able to induce l-lysine production in methylophilus methylotrophus. although lyse24 has a mutation in the middle of lyse that results in chain termination, the entire lyse locus, including the region downstream of the short open reading frame, is necessary for l-lysine production. we propose that separate polypeptides are synthesized from the lyse24 locus due to reinitiation of translation ...200617151474
structural evidence for a proton transfer pathway coupled with haem reduction of cytochrome c" from methylophilus methylotrophus.the crystal structures of the oxidized and reduced forms of cytochrome c" from methylophilus methylotrophus were solved from x-ray synchrotron data to atomic resolution. the overall fold of the molecule in the two redox states is very similar and is comparable to that of the oxygen-binding protein from the purple phototrophic bacterium rhodobacter sphaeroides. however, significant modifications occur near the haem group, in particular the detachment from axial binding of his95 observed upon redu ...200616341897
a mechanism for substrate-induced formation of 6-hydroxyflavin mononucleotide catalyzed by c30a trimethylamine dehydrogenase.experiments are described to determine the origin of the 6-hydroxyl group of 6-hydroxyfmn produced by the substrate-induced transformation of fmn in the c30a mutant of trimethylamine dehydrogenase. the conversion of fmn to 6-hydroxyfmn is carried out in the presence of h(2)(18)o and 18o(2), and the results clearly show that the 6-hydroxyl group is derived from molecular oxygen and not from water.200314592522
the influence of fluid mixing upon respiratory patterns for extended growth of a methylotroph in an air-lift fermenter.the influence of methanol dispersion and fluid mixing upon respiratory patterns observed during unlimited fedbatch growth of the methylotrophic bacterium methylophilus methylotrophus has been investigated. a concentric tube air-lift fermenter was employed for which the mixing and fluid circulation patterns have been well characterized. respiratory quotients showed a marked dependence upon the position in the vessel at which methanol was injected, the volumetric rate of such methanol addition, th ...198418553437
characterization of the l-lysine biosynthetic pathway in the obligate methylotroph methylophilus methylotrophus.the l-lysine biosynthetic pathway of the gram-negative obligate methylotroph methylophilus methylotrophus as1 was examined through characterization of the enzymes aspartokinase (ak), aspartsemialdehyde dehydrogenase, dihydrodipicolinate synthase (ddps), dihydrodipicolinate reductase, and diaminopimelate decarboxylase. the ak was inhibited by l-threonine and by a combination of l-threonine and l-lysine, but not by l-lysine alone, and the activity of ddps was moderately reduced by l-lysine. in an ...200415277749
mmei: a minimal type ii restriction-modification system that only modifies one dna strand for host protection.mmei is an unusual type ii restriction enzyme that is useful for generating long sequence tags. we have cloned the mmei restriction-modification (r-m) system and found it to consist of a single protein having both endonuclease and dna methyltransferase activities. the protein comprises an amino-terminal endonuclease domain, a central dna methyltransferase domain and c-terminal dna recognition domain. the endonuclease cuts the two dna strands at one site simultaneously, with enzyme bound at two s ...200818931376
identification of acetate- or methanol-assimilating bacteria under nitrate-reducing conditions by stable-isotope probing.stable-isotope probing (sip) was used to identify acetate- or methanol-assimilating bacteria under nitrate-reducing conditions in activated sludge. a sludge sample obtained from wastewater treatment systems was incubated in a denitrifying batch reactor fed with synthetic wastewater containing [(13)c]acetate or [(13)c]methanol as the main carbon source and nitrate as the electron acceptor. we analyzed how growth of bacterial populations was stimulated by acetate or methanol as the external carbon ...200616897304
phage mu-driven two-plasmid system for integration of recombinant dna in the methylophilus methylotrophus genome.a phage mu-driven two-plasmid system for dna integration in escherichia coli genome has been adjusted for methylophilus methylotrophus. constructed helper plasmids with broad-host-range replicons carry thermo-inducible genes for transposition factors mua and mub. integrative plasmids that are only replicated in e. coli could be mobilized to m. methylotrophus and contained mini-mu unit with a short terminus of mu dna, mu-attl/r. mini-mu unit was integrated in the m. methylotrophus genome via mobi ...200818820908
aromatic amino acid auxotrophs constructed by recombinant marker exchange in methylophilus methylotrophus as1 cells expressing the arop-encoded transporter of escherichia coli.the isolation of auxotrophic mutants, which is a prerequisite for a substantial genetic analysis and metabolic engineering of obligate methylotrophs, remains a rather complicated task. we describe a novel method of constructing mutants of the bacterium methylophilus methylotrophus as1 that are auxotrophic for aromatic amino acids. the procedure begins with the mu-driven integration of the escherichia coli gene arop, which encodes the common aromatic amino acid transporter, into the genome of m. ...201019880640
molecular cloning of the dna gyrase genes from methylovorus sp. strain ss1 and the mechanism of intrinsic quinolone resistance in methylotrophic bacteria.the genes encoding the dna gyrase a (gyra) and b subunits (gyrb) of methylovorus sp. strain ss1 were cloned and sequenced. gyra and gyrb coded for proteins of 846 and 799 amino acids with calculated molecular weights of 94,328 and 88,714, respectively, and complemented escherichia coli gyra and gyrb temperature sensitive (ts) mutants. to analyze the role of type ii topoisomerases in the intrinsic quinolone resistance of methylotrophic bacteria, the sequences of the quinolone resistance-determini ...200516404155
isolation of auxotrophic mutants of methylophilus methylotrophus by modified-marker exchange.a method for stabilizing a transposon (tn5) has been developed which allows the isolation of stable auxotrophic mutants of methylophilus methylotrophus asi. insertion of tn5 into a cloned m. methylotrophus asi dna fragment encoding anthranilate synthase followed by transfer of the vector with the modified trpe gene to m. methylotrophus asi resulted in unstable auxotrophs among the recombinants. deletion of is50r, which encodes transposase production from tn5, stabilized the transposon after mobi ...198816347531
probing the dynamic interface between trimethylamine dehydrogenase (tmadh) and electron transferring flavoprotein (etf) in the tmadh-2etf complex: role of the arg-alpha237 (etf) and tyr-442 (tmadh) residue pair.we have used multiple solution state techniques and crystallographic analysis to investigate the importance of a putative transient interaction formed between arg-alpha237 in electron transferring flavoprotein (etf) and tyr-442 in trimethylamine dehydrogenase (tmadh) in complex assembly, electron transfer, and structural imprinting of etf by tmadh. we have isolated four mutant forms of etf altered in the identity of the residue at position 237 (alphar237a, alphar237k, alphar237c, and alphar237e) ...200818407658
community structures and activities of nitrifying and denitrifying bacteria in industrial wastewater-treating biofilms.the bacterial community structure, in situ spatial distributions and activities of nitrifying and denitrifying bacteria in biofilms treating industrial wastewater were investigated by combination of the 16s rrna gene clone analysis, fluorescence in situ hybridization (fish) and microelectrodes. these results were compared with the nitrogen removal capacity of the industrial wastewater treatment plant (iwtp). both nitrification and denitrification occurred in the primary denitrification (pd) tank ...200616477661
stable carbon isotope fractionation during degradation of dichloromethane by methylotrophic bacteria.stable carbon isotope fractionation during dichloromethane (dcm) degradation by methylotrophic bacteria was investigated under aerobic and nitrate-reducing conditions. the strains studied comprise several hyphomicrobium strains, methylobacterium, methylopila, methylophilus and methylorhabdus spp. that are considered to degrade dcm by a glutathione (gsh)-dependent dehalogenase enzyme system in the initial step. the stable carbon isotope fractionation factors (alphac) of the strains varied under a ...200616343330
l-lysine biosynthetic pathway of methylophilus methylotrophus and construction of an l-lysine producer.previously, we showed that the enzymes aspartokinase (ak) and dihydrodipicolinate synthase (ddps), which are involved in l-lysine biosynthesis in the gram-negative obligate methylotroph methylophilus methylotrophus as1, were inhibited by allosteric effectors, including l-lysine. to elucidate further the regulation of l-lysine biosynthesis in m. methylotrophus, we cloned the genes encoding three other enzymes involved in this pathway, l-aspartate-beta-semialdehyde dehydrogenase, dihydrodipicolina ...200616483680
disruption of metf increased l-lysine production by methylophilus methylotrophus from methanol.methionine auxotrophic mutants of methylophilus methylotrophus as1 expressing a mutant form of dapa (dapa24) encoding a dihydrodipicolinate synthase desensitized from feedback inhibition by l-lysine, and mutated lyse (lyse24) encoding the l-lysine exporter from corynebacterium glutamicum 2256, produced higher amounts of l-lysine from methanol as sole carbon source than did other amino acid auxotrophic mutants. especially, the m. methylotrophus 102 strain, carrying both dapa24 and lyse24, produce ...200818460806
identification and cloning of a gene encoding dichloromethane dehalogenase from a methylotrophic bacterium, bacillus circulans wz-12 cctcc m 207006.the gene dehala encoding a novel dichloromethane dehalogenases (dehala), has been cloned from bacillus circulans wz-12 cctcc m 207006. the open reading frame of dehala, spanning 864 bp, encoded a 288-amino acid protein that showed 85.76% identity to the dichloromethane dehalogenases of hyphomicrobium sp. gj21 with several commonly conserved sequences. these sequences could not be found in putative dichloromethane (dcm) dehalogenases reported from other bacteria and fungi. dehala was expressed in ...200919277720
the interaction of trimethylamine dehydrogenase and electron-transferring flavoprotein.the interaction between the physiological electron transfer partners trimethylamine dehydrogenase (tmadh) and electron-transferring flavoprotein (etf) from methylophilus methylotrophus has been examined with particular regard to the proposal that the former protein "imprints" a conformational change on the latter. the results indicate that the absorbance change previously attributed to changes in the environment of the fad of etf upon binding to tmadh is instead caused by electron transfer from ...200515760891
improvement of l-lysine production by methylophilus methylotrophus from methanol via the entner-doudoroff pathway, originating in escherichia coli.to improve the amino acid production by metabolic engineering, eliminating the pathway bottleneck is known to be very effective. the metabolic response of methylophilus methylotrophus upon the addition of glucose and of pyruvate was investigated in batch cultivation. we found that the supply of pyruvate is a bottleneck in l-lysine production in m. methylotrophus from methanol as carbon source. m. methylotrophus has a ribulose monophosphate (rump) pathway for methanol assimilation, and consequent ...200818838820
enhancement of l-lysine production in methylotroph methylophilus methylotrophus by introducing a mutant lyse exporter.the obligate methylotroph methylophilus methylotrophus as1 expressing a mutant form of dapa (dapa24) encoding a dihydrodipicolinate synthase desensitized from feedback inhibition by l-lysine could secrete l-lysine into the medium, but also maintained a high concentration of intracellular l-lysine. to improve the yield from excretion, we attempted to introduce an l-lysine/l-arginine exporter (lyse) from corynebacterium glutamicum 2256 into m. methylotrophus. we were unable to stably transform m. ...200616870294
spatio-temporal niche separation of planktonic betaproteobacteria in an oligo-mesotrophic lake.we investigated the diversity of planktonic betaproteobacteria and the seasonal population changes of betaproteobacterial taxa in an oligo-mesotrophic lake (piburger see, austria). focus was put on the vertical distribution of the investigated populations and on differences between their respective cell fractions with apparent amino acid incorporation. on average, 66% of betaproteobacterial cells and 73% of their diversity could be attributed to four clades within three lineages that were furthe ...200818430016
life without light: microbial diversity and evidence of sulfur- and ammonium-based chemolithotrophy in movile cave.microbial diversity in movile cave (romania) was studied using bacterial and archaeal 16s rrna gene sequence and functional gene analyses, including ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco), soxb (sulfate thioesterase/thiohydrolase) and amoa (ammonia monooxygenase). sulfur oxidizers from both gammaproteobacteria and betaproteobacteria were detected in 16s rrna, soxb and rubisco gene libraries. dna-based stable-isotope probing analyses using 13c-bicarbonate showed that thiobacill ...200919474813
functional analysis of mmei from methanol utilizer methylophilus methylotrophus, a subtype iic restriction-modification enzyme related to type i enzymes.mmei from methylophilus methylotrophus belongs to the type ii restriction-modification enzymes. it recognizes an asymmetric dna sequence, 5'-tccrac-3' (r indicates g or a), and cuts both strands at fixed positions downstream of the specific site. this particular feature has been exploited in transcript profiling of complex genomes (using serial analysis of gene expression technology). we have shown previously that the endonucleolytic activity of mmei is strongly dependent on the presence of s-ad ...200918997032
medium composition suitable for l-lysine production by methylophilus methylotrophus in fed-batch cultivation.l-lysine production was investigated in fed-batch fermentation using l-lysine producer of methylophilus methylotrophus. by the addition of nutrient composition, containing l-methionine, k(2)hpo(4), nah(2)po(4), cuso(4).5aq, mnso(4).5aq, znso(4).7aq, fecl(3), mgso(4).7aq and cacl(2).2aq, in the feed medium, cell growth could be maintained through the cultivation, and l-lysine production reached to 7.86 g. in addition, the effect of counter ion for nh(4)(+) (cl(-), so(4)(2-), glutamate, succinate ...200819134554
methylophilus rhizosphaerae sp. nov., a restricted facultative methylotroph isolated from rice rhizosphere soil.three facultative methylotrophic bacterial strains, designated cbmb127(t), cbmb145 and cbmb147, were isolated from the rhizosphere soil of rice and characterized. the strains produced indole-3-acetic acid and siderophores, had 1-aminocyclopropane-1-carboxylate deaminase activity and sulfur oxidation property and also methanol dehydrogenase. phylogenetic analysis based on the 16s rrna and methanol dehydrogenase (mxaf) gene sequences showed that methylophilus methylotrophus was their close relativ ...200919628595
methanol removal efficiency and bacterial diversity of an activated carbon biofilter.motivated by the need to establish an economical and environmentally friendly methanol control technology for the pulp and paper industry, a bench-scale activated carbon biofiltration system was developed. this system was evaluated for its performance in removing methanol from an artificially contaminated air stream and characterized for its bacterial diversity over time, under varied methanol loading rates, and in different spatial regions of the filter. the biofilter system, composed of a nove ...200919665889
[stearic acid methyl ether: a new extracellular metabolite of the obligate methylotrophic bacterium methylophilus quaylei].methyl esters of fatty acids, free fatty acids, and hydrocarbons were found in the culture liquid and in the cellular lipids of the obligate methylotrophic bacterium methylophilus quaylei under optimal growth conditions and osmotic stress. the main extracellular hydrophobic metabolite was methyl stearate. exogenous free fatty acids c16-c18 and their methyl esters stimulated the m. quaylei growth and survivability, as well as production of exopolysaccharide under osmotic and oxidative stress, pla ...201020391761
fluorescence lifetimes of tyrosine residues in cytochrome c'' as local probes to study protein unfolding.time-resolved fluorescence spectroscopy was used to show that multiple tyrosine residues of a protein can serve as localized probes of structural changes during thermal unfolding. cytochrome c'' from methylophilus methylotrophus, which has four tyrosine residues, was chosen as a model protein. the procedure involved, first, the assignment of the experimental decay times to the tyrosine residues, followed by the interpretation of the changes in the decay times and pre-exponential coefficients wit ...200919249841
methylophilus flavus sp. nov. and methylophilus luteus sp. nov., aerobic, methylotrophic bacteria associated with plants.novel yellow, obligately methylotrophic and restricted facultatively methylotrophic bacteria, respectively designated strains ship(t) and mim(t), with the ribulose monophosphate pathway of c(1) assimilation are described. cells were strictly aerobic, gram-negative, asporogenous, non-motile rods that multiply by binary fission, were mesophilic and neutrophilic and synthesized indole-3-acetic acid and exopolysaccharide. the predominant cellular fatty acids were c(16 : 0) and c(16 : 1). the major u ...201020023062
enrichment and cultivation of pelagic bacteria from a humic lake using phenol and humic matter additions.individual bacterial populations are known to respond differently toward substrate availability. to test how the availability of either pure phenol or natural humic matter (hm) selects for specific pelagic bacteria phylotypes from a humic lake (lake grosse fuchskuhle, northeastern germany), we used culture-dependent and -independent approaches. using a batch approach, the bacterial community composition (bcc) differed depending on both the quantity and the quality of added substrates. using a di ...201020459514
crystal structure of histamine dehydrogenase from nocardioides simplex.histamine dehydrogenase (hadh) isolated from nocardioides simplex catalyzes the oxidative deamination of histamine to imidazole acetaldehyde. hadh is highly specific for histamine, and we are interested in understanding the recognition mode of histamine in its active site. we describe the first crystal structure of a recombinant form of hadh (hadh) to 2.7-a resolution. hadh is a homodimer, where each 76-kda subunit contains an iron-sulfur cluster ([4fe-4s](2+)) and a 6-s-cysteinyl flavin mononuc ...201020538584
endosymbionts of acanthamoeba isolated from domestic tap water in korea.in a previous study, we reported our discovery of acanthamoeba contamination in domestic tap water; in that study, we determined that some acanthamoeba strains harbor endosymbiotic bacteria, via our molecular characterization by mitochondrial dna restriction fragment length polymorphism (mt dna rflp). five (29.4%) among 17 acanthamoeba isolates contained endosymbionts in their cytoplasm, as demonstrated via orcein staining. in order to estimate their pathogenicity, we conducted a genetic charact ...200919967080
biphenyl-metabolizing bacteria in the rhizosphere of horseradish and bulk soil contaminated by polychlorinated biphenyls as revealed by stable isotope probing.dna-based stable isotope probing in combination with terminal restriction fragment length polymorphism was used in order to identify members of the microbial community that metabolize biphenyl in the rhizosphere of horseradish (armoracia rusticana) cultivated in soil contaminated with polychlorinated biphenyls (pcbs) compared to members of the microbial community in initial, uncultivated bulk soil. on the basis of early and recurrent detection of their 16s rrna genes in clone libraries construct ...200919700551
methylophilus glucosoxydans sp. nov., a restricted facultative methylotroph from rice rhizosphere.two restricted facultative methylotrophic strains, designed bt and p, were isolated from the rice roots and characterized. the isolates were strictly aerobic, gram negative, asporogenous, motile rods multiplying by binary fission, mesophilic and neutrophilic, syntheized indole-3-acetate. the cellular fatty acid profile is dominated by c16:0, c16:1?7c and 2-oh c16:0 fatty acids. the major ubiquinone is q8. the predominant phospholipids were phosphatidylethanolamine and phosphatidylglycerol. cardi ...201121378135
the enzymatic reaction-induced configuration change of the prosthetic group pqq of methanol dehydrogenase.methanol dehydrogenase is a heterotetrameric enzyme containing the prosthetic group pyrroloquinoline quinone (pqq), which catalyzes the oxidation of methanol to formaldehyde. the crystal structure of methanol dehydrogenase from methylophilus w3a1, previously determined at high resolution, exhibits a non-planar configuration of the pqq ring system and lends support for a hydride transfer mechanism of the enzymatic reaction catalyzed by the enzyme. to investigate why pqq is in the c5-reduced form ...201121356200
enrichment and cultivation of pelagic bacteria from a humic lake using phenol and humic matter additions.abstract individual bacterial populations are known to respond differently toward substrate availability. to test how the availability of either pure phenol or natural humic matter (hm) selects for specific pelagic bacteria phylotypes from a humic lake (lake grosse fuchskuhle, northeastern germany), we used culture-dependent and -independent approaches. using a batch approach, the bacterial community composition (bcc) differed depending on both the quantity and the quality of added substrates. u ...201020100184
bacterial communities constructed in artificial consortia of bacteria and chlorella vulgaris.we established artificial consortia of bacteria inoculated from soil and a green alga, chlorella vulgaris nies-227. the bacteria and the alga were mixed in a tube or partitioned in a dialysing culture vessel, and the bacterial composition was examined after cultivation. the community of bacteria formed in the consortia included those phylogenetically closely related to the genera phenylobacterium, brevundimonas, phyllobacterium, afipia, sphingomonas, sandaracinobacter, ramlibacter, ralstonia, ce ...201021576850
highly selective ligand binding by methylophilus methylotrophus cytochrome c''cytochrome c'' (cyt c'') from methylophilus methylotrophus is unusual insofar as the heme has two axial histidine ligands in the oxidized form but one is detached when the protein is reduced. despite cyt c'' having an axial site available for binding small ligands, we show here that only no binds readily to the ferrous cyt c''. binding of co, as well as cn(-), on the other hand requires considerable structural reorganization, or reduction of the disulfide bridge close to the heme. standard free ...201121599015
application of the bacteriophage mu-driven system for the integration/amplification of target genes in the chromosomes of engineered gram-negative bacteria--mini review.the advantages of phage mu transposition-based systems for the chromosomal editing of plasmid-less strains are reviewed. the cis and trans requirements for mu phage-mediated transposition, which include the l/r ends of the mu dna, the transposition factors mua and mub, and the cis/trans functioning of the e element as an enhancer, are presented. mini-mu(lr)/(ler) units are mu derivatives that lack most of the mu genes but contain the l/r ends or a properly arranged e element in cis to the l/r en ...201121698377
phyllosphere bacterial communities of trichome-bearing and trichomeless arabidopsis thaliana leaves.this study aimed to investigate whether the presence of trichomes as conspicuous physical attributes of the leaf surface affects the microbial community composition on arabidopsis thaliana leaves. the a. thaliana ecotype col-0 and its trichomeless gl1 mutant were grown in growth cabinets under climate-controlled conditions. the gl1 mutant showed a similar wax composition as the col-0 wild type with slightly reduced amounts of c(29), c(31) and c(33) alkanes by gc/ms and gc/fid analyses. 120 bacte ...201122080429
diversity and biogeography of selected phyllosphere bacteria with special emphasis on methylobacterium spp.on the basis of cultivation-dependent (isolation on mineral salt medium supplemented with 0.5% methanol) and -independent (dgge analysis) methods, we investigated the influence of the host plant species trifolium repens and cerastium holosteoides, three geographic locations and the land-use types meadow, mown pasture and pasture on the abundance and community composition of selected phyllosphere bacteria with emphasis on methylobacterium species. methylobacterium abundance was significantly high ...201122000032
an integrated proteomics/transcriptomics approach points to oxygen as the main electron sink for methanol metabolism in methylotenera mobilis.methylotenera species, unlike their close relatives in the genera of methylophilus, methylobacillus and methylovorus neither exhibit the activity of methanol dehydrogenase, nor possess mxafi genes encoding this enzyme, yet they are able to grow on methanol. in this work, we integrated two genome-wide -omics approaches, shotgun proteomics and shotgun transcriptome sequencing (rna-seq) of methylotenera mobilis jlw8 to identify genes and enzymes potentially involved in methanol oxidation, with spec ...201121764938
Impact of anthracene addition on microbial community structure in soil microcosms from contaminated and uncontaminated sites.This paper aims to investigate the impact of anthracene addition on microbial community in agricultural soil irrigated with tap water or reclaimed wastewater.201122108422
Changes in bacterial community of anthracene bioremediation in municipal solid waste composting soil.Polycyclic aromatic hydrocarbons (PAHs) are common contaminants in a municipal solid waste (MSW) composting site. Knowledge of changes in microbial structure is useful to identify particular PAH degraders. However, the microbial community in the MSW composting soil and its change associated with prolonged exposure to PAHs and subsequent biodegradation remain largely unknown. In this study, anthracene was selected as a model compound. The bacterial community structure was investigated using termi ...201121887852
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